SeedViewer Subsystem

SEED Viewer Subsystem Page

Use the 'This Subsystem' menu in the green bar at the top of the page to view the 'Populated Subsystem' spreadsheet or to 'View Notes' for this susbystem.
or to return to the 'Overview'.

Overview

On the top, right of the page a box contains the statistics for this subsystem including the

number of functional roles, total number of genomes, and the number of genomes where this subsystem

is present,not present or is still a work in progress.

The username of annotator who is responsible for the subsystem is listed.

Diagram

The diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors.

The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem.

Functional Roles Table

This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.

When present the entry in the EC column links to KEGG.

In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction

or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page

which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO.

Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because

they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.

If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu

to highlight the roles in the table that define internal pathways of the subsystem.

Populated Subsystem

By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.

The taxonomy ID in the organism column is linked to an Organism page in the SEED Viewer.

An explanation of number in the Variant column is found by selecting 'View Notes' under the 'This Subsystem' menu in the green bar at the top of the page.

At the bottom of the page, checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress' and clicking the 'Refresh populated subsystem' button, will update the spreadsheet with these genomes.

Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.

Use the 'Collapse/Expand Group Aliases' button to combine or separate columns that are in the same group.(not yet implemented)

Hovering over any element in a cell will display the SEED ID(s) of the gene(s) it contains .

Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.

A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.

A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.

A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.

Notes

The notes page contains explanations of the variant codes, references and additional information about this subsystem.